Since he doesn't have a EU spec bike or an early 2004 950 that stuff doesn't really apply per the the HOW stuff quoted.
The EPC can be unchecked via Tune ECU if it was enabled, the several newer 990's I have looked at the EPC wasn't enabled. I have the 2012 "R" map on my 2010 990R without and of his complaints. It shouldn't be fuel filters with that low mileage, maybe the side stand is bouncing around and triggering the safety switch.
A mangy man chasing a cautionary tale
KTM 990R 500EXC